The story operates through Arcs, which can vary in length. Sometimes it is difficult to pinpoint where one Arc ends and another Arc begins, though it is usually after a major event, such as a big battle. For simplicity's sake, the earliest point which an arc plot is mentioned is listed.

J-Team Assemble Saga

Chapter 1: Get That Guy Out of My Continuity

The heroes meet and greet each other at an airport to Sinnoh, intending to go to Snowpoint Temple. Mewtwo contacts them, and they then take it upon themselves to search and destroy known rapist David of Pokémon Story infamy. When defeated, David explodes, and we learn that he was a puppet of Missingno. Mewtwo says that the only way to defeat it is with Giratina, Palkia, and Victini.

Chapter 2: Explosions and Dimensions and Monsters, Oh My!

Missingno turns Canalave into bunch of eggs. The heroes continue to trek towards Snowpoint and reach Eterna. They Rendezvous with Professor Oak and learn that Victini is a Nuke. Cynthia, who happens to own a Giratina, is called on for help, and the group treks up to Spear Pillar in order to convince Palkia to help. With all three Legendary Pokemon gathered, Missingno appears, and is banished to another Dimension. Everyone else gets sucked into the other Dimension as well, and Anom and Jane are both bolted to the wall and unable to help. Eventually, the bridge that connects the two dimensions is broken, and everyone is spat back out into Mt. Coronet, safe and sound. Also Palkia gave Gamer a mechanical toe.

Chapter 3: The Snowpoint Giant

The journey to Snowpoint continues, and they soon discover Regigigas underneath Snowpoint Temple. With the help of the three Regis, Regigigas is revived, and it and Jane become fast friends. Once Regigigas is out of the temple with its 'children', a Team Rocket signal gets intercepted by Jane, and she and Tagg seek to destroy the operation before it can go anywhere. Oh, and Dialga's there too. Dialga is used to blow up the Team Rocket base, and the Admin gets defeated by the Golems, and then decides that he doesn't want to see Team Rocket fall, so he dives into the lava pit. Sissy.

Chapter 4: Glitch City

The group decides to leave the Battle Zone where the lava pit was and go to Canalave. New Guy Lukeshows up and wants to follow. They then get attacked by a reanimated Aerodactyl skeleton. The skeleton claims to be Missingno before it gets destroyed by a hyper beam. The group them flies over to Canalave, which takes about an hour, and find that it is surrounded in a giant cloud. A Nurse Joy Gone Mad flies around on a Fearow and creeps the heck out of everybody, then Missingno (who is now a purple blob-orb) tries to take over Jane's body. Fighting ensues, Jane is knocked out, and Daisy's Charizard dies. Eventually, everyone discovers that it's just some guy named Pies who wanted to revive a Rayquaza fossil and own a legend. He gets sent to jail and his pokemon are taken away and released.

Chapter 5: What Now?

A new building erects itself from the ocean near the presumably rebuilt Canalave city. The heroes go in. They are then subject to a number of Mind Screws, such as; Jane and Gamer's Pokemon getting genderbent, Luke and his Meganium getting sucked into Sonic Colors, Jane and Palkia switching bodies, Tagg's pokemon reverting to their first stages, Gamer turning into a Snivy, Slouch getting stuck to the ceiling and his Pokémon shrunk to the size of ants, Kyogre showing up with a rocket tied to its belly, and Mewtwo in a woman's one-piece bathing suit and reading the instruction manual to Pokemon Platinum. The only real good that comes out of this is that we learn that Palkia is female.

Chapter 7: Super Contests

A Pokémon trainer known as DS comes to Canalave after hearing rumours of the strange things that happened there, and ends up meeting up with and joining the group. The gang goes over to Sandgem Town and talks to Professor Rowan about the Pokemon Only World. Once they are done there they run off to Hearthome and mess with the Contest. Gamer and Pentigan participate in the contest but lose to Chuggaaconroy. Pretty much nothing but Filler. Well, except for Palkia getting possessed by Missingno, but that's irrelevant at this point.

Pokémon Mystery Dungeon

Chapter 8: Mysterious Bodies and New Surroundings.

The gang go to Fullmoon island and summons Palkia to take three of their Pokemon to the Poekmon-only world. However, Missigno is still possesing Palkia, and sends all the human Trainers there too. Upon entering the world, the group is seperated from one another and turn into Pokemon: Jane is a Ralts, Luke is a Totodile, Anom is an Anorith, Tagg is a Mudkip, Gamer is a Pikachu, Pentigan is a Lopunny, Daisy is a Piplup, Slouch is an Ursaring, and DS is an Eevee. In addition to all this, Jane, Luke, and Tagg all gain amnesia. Luckly for all involved, Tagg recovered shortly after awakening, and both he and Gamer were Genre Savvy enough to get the other's memories back, then train each other by fighting. The next morning, a Rescue Team from the nearby Treasure Town is sent out to investigate the noises made by the fight, and "save Jane from her kidnappers". The group gives chase and everyone comes to an understanding.

Chapter 9: No Time!

The group meets with Guildmaster Wigglytuff and decide to go out and find Uxie, Mesprit and Azelf, then to find Dusknoir (No relation to the Dusknoir involved in PMD's original story.) to get back to the Human World. Jane's Gallade appears through a portal and helps Jane, Anom and Gamer get to Uxie and explain to her what's happening. While they're doing that, Daisy goes back to Fullmoon Island through Gallade's portal to keep the Regis company while they monitor Gallade's Bungee Cord (long story). Then Missingno comes along and possesses the Regis. Palkia is on the search for Uxie, and things become more high stakes. Eventually, everyone but Jane and her Gallade make it back to the Human World. Things are starting to become bleak...

Chapter 10: Bye-bye, Missingno!

Once the group has ammased their army of Legendaries, Mewtwo teleports everyone to Missigno's stronghold. The group has to call out all their Pokemon to keep the shadow creatures at bay. This is further complicated when Missigno manifests the group's collective fears, which distract the group and sap away their will to fight. However, it doesn't work.Missingno gets crushed underneath a boat full of random Legendaries, exposing his core. Inside is A severely deformed, decaying prototype of Mewtwo, kept alive by a supercomputer. Mewtwo breaks the machine, and both Missigno's physical and data forms are destroyed forever. The group buries him and then get turned back into humans. After turning back into humans, Filler ensues until March 6th, when they will all finally go to Unova. Jane goes back home to Lavaridge with Tagg, Luke, Anom and Daisy, Pentigan goes to Lavaridge of his own accord, DS and Slouch stay in Sinnoh and Gamer plays Giratina the First in mini-golf. A number of other things occur such as mostly everyone getting visions from the Unown, Anom fighting an evil Tentacruel/Old Man hybrid, Jane having a tantrum over a change Porygon2 made to the recorded video and a new mission from Pentigan, finding the Sabot Warriors...

Unova

Chapter 11: Getting our Bearings

We're in Unova now! But that's not important. What is important is that Jane's new Servine, Rebecca, runs away, Virizion takes Rebecca to the other Sabot Warriors, the group chases them and finds them in Undella Town with Cynthia and her Giratina. Then Steven Stone shows up and blows up Undella Town with his Helicopter. It turns out, he was possessed by Missingno's twin brother, 'M. 'M echoes out a warning to the others before Steven is hospitalized. The group takes this is stride and decide to finish gathering badges. The team have spent some time fighting Elesa, before Virizion shows up being chased by Clay's Excadrill. Virizion is badly injured, and the Excadrill manages to cause massive damage to the Amusement Park in Nimbasa. The group gets rid of the Excadrill, but Virizion is in need of intensive care...

Chapter 12: Raised By Dragons

Virizion is healed after about three days of being hospitalized. Wolf relays to the others that Clay has the Terracotta Warrior, Terrakion. Iris has told him that Keldeo, the Fourth Warrior, is being protected in Opelucid City, but Virizion says that Keldeo was stolen at the same time as Terrakion. Iris actually shows up, in-the-flesh, making Daisy panic and chuck a Masterball at Virizion. Iris then chases Daisy around for the Masterball, eventually turning into a half-haxorus-half-Iris monster because of the influence of 'M. IriM attacks the group with her Haxorus and Fraxure, but is defeated, and 'M escapes. Virizion is released from the Masterball almost immediately and promises to travel with the group as repayment for "being granted [her] freedom".

Chapter 13: Vs. Cowboy

The group decides to split up, one travelling to Anville town to draw Clay away from the gym, while the other goes to Driftveil city to rescue Keldeo and Terrakion while Clay is away. However, on the way there, the Anville group run into some trouble when they accidentally fly too close to the habitat of some wild Zoroark. They manage to escape, but Anom is seriously injured and his Yanmega goes missing in the chaos. The Anville group fights a 50-foot Clay, possesed by 'M. To stop him' Gamer's Charmander stubs his toe to stun him, while Skyla's Swoobat and Kratos possess him to drive away 'M's influence. In Driftveil City, Jane, Luke, Tagg, DS and Virizion rescue Terrakion and Keldeo out from Clay's gym.

Chapter 14: To Opelucid!

After rescuing Keldeo and Terrakion, the two groups decide to meet up again at Mistralton city. After having mostly recovered from his injuries, Anom goes back to the forest to look for Yanmega. Crewe comes along, and catches the leader of the Zoroark. Wolf then helps Anom look for Yanmega, only to discover that Yanmega has been killed by the Zoroark pack. After meeting up again in Mistralton city, the group discover what has happened to the children from the daycare, giving them another very good reason to want to destroy 'M. Everyone starts on a trek to Opelucid City, challenging gyms along the way. Weird things happen inside Twist mountain, some of which later become important plot points. And something seems to be wrong with Jane.

Chapter 15: Nightmares in the Dream World

The group eventually makes it to the Pokémon League. They discover that the Elite Four are all in a Convenient Coma. Jane goes evil. Everyone else gets stuck in the Dream World, where they must face their own inner demons. Also Ghetsis is there with a bunch of Plasmorons. Everyone gets into an epic fight full of epic. At least until...

Chapter 16: How We Got Here In The First Place

Chapter 17: Now, Where Were We?

The battle at the Pokémon League continues. Having gained a mental connection after the events at Twist mountain, Anom attempts to get through to Jane. Unfortunatly, Jane can't find the strength to fight off 'M's possession, and during the battle, Wolf is killed by a shadow ball attack. Things get even worse when Daisy's Zoroark accidentally causes the death of Jane, and Ghetsis manages to escape. Realizing the battle is pretty much over, the trainers are left to mourn the apparent deaths of their friends. Meanwhile, the spirits of Jane and Wolf find themselves in an empty void. Jane's Gallade shows up and asks Jane to come with him to meet with Arceus, but Wolf is unable to see Gallade and tells her to leave without him. Outside the League building, Pentigan's helicopter is shot down by 'M, and Pentigan discovers the true identity of the mysterious old man before waking up back in the real world, and Arceus is convinced to bring Jane and Wolf back to life. Back in the real world, DS is surprised when it appears that Wolf is breathing again, and asks him to wake up, which he does. Jane and Gallade free Jane's Pokémon from their Mind Control before Jane goes back to her body.

Chapter 18: The End (Part one)

After Jane and Wolf both return to life, the group decides that it is time to take down 'M's data core, and they head over to Team Plasma's castle to confront it. Exploring until they reach the end of the castle, they must face 'M and its army of shiny Charizard. Eventually, the group manages to take down 'M's data half. Alder and the shiny Charizard are free from 'M's control, but the Charizard do not return to their original forms. The group decides to head to the Grey ruins to take down 'M once and for all.

Chapter 19: The End (Part two)

After making the trip through Black city and White forest, and finding their way to the Grey ruins, the group must fight 'M organic half. Everything 'M puts the group through while travelling through the area proves to be too much for Jane and she chooses to escape the area. The group minus Jane fight off 'M, which transports them to Glitch city. Anom makes a Heroic Sacrifice and manages to destroy 'M's anti-legendary shield, allowing the legendary Pokémon to join the fight and finish off 'M once and for all.

Chapter 20: In the Aftermath

'M has been defeated, and the children from the daycare are returned to normal. However, the loss of Anom and the tension between Gamer and Jane threatens to break up the group. In addition to this, Arceus blames itself for not being able to save Anom, and decides to give up its position as the deity of the world of Pokémon, much to everyone's shock. OLD MAN and his Weedle are put in charge until Arceus decides to return, and the legendary Pokémon are sent out to try to find out what happened to Anom.

Chapter 21: The Abyssal Ruins

Most of the group head over to Undella town's beach to get their minds of everything. While Jane discovers that pretty much every member of the Frillish line is insane, part of the group heads down to the underwater Abyssal Ruins in an attempt to capture Ghetsis and the Shadow triad. Much to everyone's frustration, Ghetsis and the Shadow Triad manage to escape. Also, some strange things happen on April Fools' Day, which include among other things: Gamer being turned into an android, DS becoming invisible, Wolf getting turned into a girl (again) and Jane turning into an Entei voiced by Dan Green and challenging the others to a game of Yu-Gi-Oh.

Chapter 22: The Return

It's been a week after 'M's defeat, and OLD MAN asks everyone to meet at Route 14. Arceus returns, and decides to return to his position, thanking OLD MAN for running things in its absence. The Sinnoh Lake Trio are gathering up tiny particles which were spread all over Route 14, left behind after the defeat of 'M. Once all the particles are gathered, they are assembled and reveal the unconscious form of Anom. The legendary Pokémon leave, and the group is happy to have their friend back. After Anom regains consciousness, the group explains to him what has happened after the battle against 'M.

Chapter 23: The Giant Chasm

The group decides to go after Ghetsis, who has gone to the Giant Chasm to catch Kyurem. However, they arrive too late, and discover that not only has Ghetsis captured Kyurem, but he has also turned him into a shadow Pokémon! Realizing that having a Mind of Crystal gives her a connection to Kyurem and might help bring Kyurem to his senses, DS takes the Grey orb and attempts to bring Kyurem to his senses. DS finds that the closer she gets to the ice dragon, the colder it gets. Realizing DS might have put herself in danger, Wolf decides to help her, and realizes that he too is a Mind of Crystal. However, Ghetsis orders Kyurem to freeze everyone to death, and while Kyurem is unsure of what to do, it begins charging up its Glaciate attack anyways. Thinking quickly, DS manages to finally snap Kyurem out of it by offering it a scarf. After this, Kyurem turns on Ghetsis, freezing him and finally allowing him to be arrested.

Chapter 24: Party Time!

Keldeo and his father decide to throw a party for the trainers, since they helped save the world. However, things get a bit out of control when Tornadus and Thundurus decides to spike the punch, causing several legendary Pokémon attending the party to get drunk. Palkia is one of the pokemon, and leads to the entire planet orbiting Saturn and adopting Uranus as its moon. Eventually things get fixed when Palkia gets sober, but she still has an enormous hangover the next day. During the party, it is also discovered that Slouch and Anom are Minds of Crystal as well.

Chapter 25: For All It's Worth

Gamer and Tagg go off to challenge the Pokémon League, Jane, Crewe and Anom go off to challenge some gyms, while DS, Wolf, Luke and Slouch head off to the Relic castle. Gamer and Tagg challenge the Elite Four members together, Jane, Crewe and Anom earn some badges, DS finds some TM's she needed with the help of Luke and Wolf. The Relic castle group also get into some trouble with a Cofagrigus, but manage to defeat it. Two friendly Yamask guide them through the rest of the castle, and help them find a Volcarona living deep within the castle. The Volcarona decides to join Luke's team, and everyone agrees to meet up again in Castelia City once they're all done doing whatever they were doing.

Chapter 27: Mixed Up Bodies, Mixed Up Feelings

We all go to Oblivia. Shortly after arriving, the Manaphy egg begins to hatch, and Anom takes it down to the beach. However, he is attacked by Pokémon Pinchers, who try to take the Manaphy away. Wolf, who had secretly followed Anom down to the beach, tries to help. In the middle of the chaos, the newly hatched Manaphy panics and uses heart swap, before being taken away by the Pinchers. The two soon realize that the Manaphy being stolen is not their only problem, as Manaphy's heart swap has swapped their bodies. To begin with, the two try to hide this from the group by pretending to be each other, but the group quickly catches on to the fact that something is not quite right about their friends. The group also begins working on gathering the region's legendary Pokémon in order to take down the Pinchers, with several of Oblivia's legendary Pokémon being rather... odd. Wolf and Anom do eventually tell a few members of the group what is really going on with them, but this doesn't make the situation any easier for them. Shortly after thelegendarybeasts and two of the legendarybirds of Oblivia have been gathered, DS ends up accidentally revealing Wolf and Anom's secret after the tension in the group finally becomes too much for her to handle.

Chapter 28: Where are those blasted Pinchers?

After the secret has been revealed, the peace within the group has been restored, and everyone is focusing on helping Anom and Wolf find the Manaphy so they can return to normal. The Minds of Crystal within the group find their Eon Dragons, which will be needed to get to Layuda island, where Oblivia's Zapdos is said to live. Luke and the legendary beasts of Oblivia also succeed in summoning Ho-oh. Some of the members in the group (DS, Fool and Anom) get injured on the way to Mt. Layuda, forcing the group to split up after meeting Zapdos: Part of the group goes to summon Lugia, while the others stay behind to look after the injured members of the group. After summoning Lugia, the group decides it is better to take Fool and Anom (whose injuries were more serious than DS') to a hospital to have their injuries treated than just staying inside the cave.

Chapter 29: Finishing our business in Oblivia.

After discovering that the Pinchers are hiding out at the Sky Fortress, Fool helps form a plan on how to get into the Sky Fortress so they can rescue Manaphy. With the help of the legendary Pokémon, the group manage to get inside, but things get a bit complicated. Tagg's Zweilous evolves and goes on a rampage before being calmed down, Anom and Fool get injured again, and the legendary Pokémon get a bit carried away while attacking the Sky Fortress. Luckily, the trainers manage to find Manaphy, and thanks to a group of Wailord the wild Pokémon inside the fortress are saved before the fortress blows up. Afterwards, Luke tries to help the wild Pokémon from the Sky Fortress find a new home, and thanks to the Manaphy, Wolf and Anom are finally returned to their own bodies. Once Manaphy has been released into the ocean, the group decides to get on the plane to Fiore, where our next adventure awaits.

Chapter 30: The Hunt for Red Gamer (Part one)

We go to Fiore, with several new trainers joining us. Gamer decides to go off on his own, wanting to take down Ardos and feeling that much of the weirdness the group has been put through is partially his fault. He leaves after talking to Tagg about it, leaving his Porygon 2 with him. During the travels through Fiore, the trainers end up fighting the Go-Rock Squad and their musical instruments that allow them to control Pokémon. Other things also happen, such as Rebecca the Serperior wanting to know how to be a good mother, and Jane forgiving Groudon, after he clears up a misunderstanding about something that happened ten years ago. Eventually, most of the group fights the Go-Rock Squad admins at the ruins of their old base, having to face several Tyranitar and Metagross. Eventually, the Mind Control signal from the Go-Rock Squad's instruments is cancelled out by Pentigan playing the keys of the abandoned pipe organ Gordor once used to control the legendary beasts, after one of the new trainers in the group manages to get it to work. Tagg manages to get some information out of the Go-Rock admins, discovering that Gamer has been kidnapped and brought to Almia.

Chapter 32: Full Circle

After rescuing Gamer, the group decide it is time to begin heading back to Sinnoh as the Gold Conference will begin in only a few days. Some of the people in the group decide to take some time to go sightseeing before they begin heading back to Sinnoh. Concerned by the fact that Anom has been sleeping a lot more than usual the last few days, Jane suggests that they try to find out what is causing it. They soon discover that Darkrai is behind it, having tried to enter Anom's dreams in order to give him a warning that Dialga will betray the other legendary Pokémon at some point in the near future. Some of the other trainers soon receive the same warning from some of the other legendary Pokémon. While this news understandably causes a bit of worry among the trainers, they decide to not worry about it too much for now, and focus on the upcoming tournament. And so, we return to Sinnoh, where several of the trainers reunite with some of their old team members.

The Gold Conference

Chapter 33: The Gold Conference (Part One)

After several of the trainers reunite with their old teams, everyone heads over to Jubilife city as the Gold Conference begins. Apart from the tournament battles, other things also happen, such as the group discovering they have a somewhat large fanbase. Tagg meets with some of his co-workers and beginstellingthemthestory of the group's adventures so far. Jane and Fool start working on gathering some orbs. Luke helps his new Dragonite work on his flying and battling skills. Anom gets locked in a janitor's closet by someone, and is stuck in there for two days before managing to free himself. Gamer ends up having to face Red in his second round match, and after putting a good fight, loses. Tagg and some of the other researchers also end up having to negoiate with a tribe of Cubone for the release of Tangent's Pokémon. Tagg and DS find a strange item similar to an Odd Keystone in the Sinnoh underground. A meets and befriends Shaymin. And Jane ends up having to quit the tournament and return home because of her mother's Camerupt being sick, but not before having said good-bye to everyone.

Chapter 34: The Gold Conference (Part Two)

The tournament continues. Tagg and some of the other researchers realize that the fans have secretly placed bugs on them to listen in on their conversations. Wolf and Anom decide to take advantage of this to mess with the fans' heads, and shortly afterwards, they discover that there are fanfics of the group. The other trainers also freak out a bit upon discovering this. Other things also happen, such as Cilan having his Simisage sneak into DS, Wolf and Anom's hotel room at night and dye Anom's hair green. During Tagg's tournament battle with Giovanni, some of Giovanni's henchmen attempt to sabotage the battle, leading to some of the other trainers intervening. This leads to some minor problems with the Gold Conference's judges, but luckily this is quickly resolved and Tagg can stay in the tournament. Keldeo and Keldeo I show up to watch the tournament, and DS, Tagg, Luke and Latias tell them about the group's adventure in Oblivia. Luke decides to join the PEFE, and must undergo a few tests as part of his initiation, including spending a night with the Cubone tribe Tagg, Tracer and Tangent had to deal with earlier. Fool's Archen Quetzal starts to regain part of her memory of her previous life, and it is soon discovered that she is in fact Crush's long lost friend, and the two fossil Pokémon are happy to see each other again. While still with the Cubone tribe, Luke discovers that the time in the area is somewhat messed up due to the tribe being in possession of Dialga's toothbrush.

Chapter 35: The Gold Conference (Part Three)

The tournament continues. Luke returns from the Cubone tribe, discovering that he took the wrong path when leaving and ending up returning a few days later due to the messed up time in the area. Jane is still in Hoenn, and contacts Fool, and they continue their search for the orbs, discovering that two of them are in Hoenn. A mishap with a Ditto results in Luke unwittingly becoming the biological father of a Torchic, and DS uses the human-to-Pokémon armband to evolve her Pokémon form into Espeon, only to lose control of her new form's psychic powers. Tagg's Hydreigon and Nadia the Salamence have another bad encounter, and Flare's egg hatches into a blue feathered Torchic. Gamer learns the Suefisk's real name. Anom gets into another sticky situation while helping Star with one of her deliveries. Tagg tells Silent and Tangent the rest of the story of the group's adventures. Nadia's plushie goes missing, and she eventually discovers that it has been taken by Sonny and Courtney, who hold it for ransom. The solvent needed to separate Anom and Star's hands from each other arrives, and the two are no longer stuck to each other. Slowly, but surely, the tournament starts coming to end as we get close to the final rounds. Luke's new Misdreavus, Hallow bonds with Phantom by pulling some pranks on the other Pokémon, such as pushing a bubble containing three of Luke's Pokémon down a hill. Nadia the Salamence's wing has healed, finally allowing her to fly again. Tagg discovers that he may have potential Aura powers. After showing some PEFE related flashbacks, the final battle of the tournament between Tagg and Fool finally begins, and comes to a very close match. After the battle, they are teleported to the Hall of Origin and discover that Arceus was in charge of the tournament, and presents them with their rewards for winning. Before sending them back to the arena, Arceus informs them that Suefisk has put a spell on the group's fans, and once the Suefisk has been defeated, they will return to normal.

Chapter 36: The Calm Before The Storm

The tournament is finally over. Luke and Tracer decide to go to Kanto for a week to take care of some stuff they needed to take care of. After arriving in Celadon, it does not take long before they start getting into some trouble. DS and Wolf say good-bye to their Latias, before the two Latias sisters fly back to Oblivia. After checking out of the hotel, the trainers decide to head over to DS' villa in the Resort Area, and stay there for a while. Luke, Tracer and their Pokémon get caught up in a Murkrow gang war, and eventually Tagg teleports over there with some of the others to help them out. Tracer and Luke go over to visit Kat's tribe, and Tagg teleports over to Kanto again and joins them for a little while. Jane contacts Fool again, having managed to find the orbs she was looking for, but having gotten trapped in a cave by Ariados. Fool teleports over to assist her, and once all is taken care of, the three teleport back to DS' villa. Luke and Tracer help Kat and the Cubone tribes work on the exchange program with the Cubone tribe in Sinnoh. Azelf receives a call from Giratina, and apparently receives some news that she, Uxie and Mesprit have to look into immedietly, the three of them heading over to the Distortion World. The next day, the Lake Trio fly over to the Resort Area, where they give DS some terrible news: Cyrus has escaped from the Distortion World. In order to eliminate one of their two problems, the trainers decide to defeat the Suefisk first, with Gamer realizing that the best way to lure her out is to make fun of her worst fanfics. They eventually succeed at this, and Gamer is eventually able to banish Suefisk back to the dimension she came from, where she will eventually be defeated. Realizing that there might not be much time before Dialga's betrayal, Fool decides to use the pendant she got from Arceus so she can talk to her parents. The next day, strange things happen...

Upheaval Saga

The AU Arc

Chapter 37: Lost Memories

Everything has changed. Scolipede and Artemis now rule Unova, and a resistance led by Goggles is working hard in hopes of bringing them down. None of the trainers have met, and most of them have lost their memories, with the exception of the Minds of Crystal. However, only Wolf is capable of trying to find the others, as Anom has been imprisoned by Scolipede and Artemis, Slouch has turned back into an NPC, and DS appears to be no where to be found. It's not only people though — Sinnoh is now a wrecked land!

All of the trainers keep their abilityto speak to Pokémon, which tips them off to the fact that something is not right. Fool and Mezzo are working for Scolipede and Artemis. Tagg regains his memories thanks to the power of the Adamant Orb, and he tries to help Tracer regain his. Luke started out with a Cyndaquil instead of a Totodile, while Lake keeps his memory and sets out to find him. Some of Luke's other Pokémon, as well as some of Tracer's Pokémon end up in different places. Pentigan started out with a Swablu instead of a Buneary in this timeline. Every joins the resistance, along with Sunny, who is an Espeon in this timeline. Crewe hasn't left the family business. Gamer is working for the Greedy Golett, who is now a Golurk in this timeline. Something strange happens at PEFE. And that is not even all of them.

Lake finds himself back in Newbark Town, where Meganium informs him that Luke had chosen Cyndaquil in this timeline instead of him. He doesn't take it well. He soon realizes that the entire timeline has changed, and sets out to find Luke. While in Unova, the rest of Luke's team is ambushed by a team of bug types, but are rescued by Unite, who is a resistance member in this timeline. Unite regains his memories shortly afterwards, and takes Luke's other Pokémon back to the resistance base. Star accidentally discovers that the gym leader Elesa has been replaced by a Zoroark and a Chatot impersonating her, creating some chaos in the process as the Zoroark attempts to get away when Every shows up. In Kanto, Tagg has to awaken Tracer's memories, and once that happens they decide to try to weaken Artemis and Scolipede's hold on Kanto. Lake manages to find and awaken Luke in Azalea, Gamer decides to try take on the Gym Leaders on his own, and Silent is sending Nidos at PEFE in exchange for combat materials for the Colony.

Chapter 38: Downward Spiral

After losing their base, the Resistance now have to find a new base, among other things. The Resistance has ended up in Sinnoh, and begin discussing with the Cubone tribe what to do. Unite and Luke's team discover that the white stone Unite has been carrying around is actually Reshiram, who has not yet been awakened in this timeline. Tagg and Tracer begin working on exposing the Zoroark impersonating the Kanto Gym Leaders, in hopes of weakening Scolipede and Artemis' hold on the region. Wolf also manages to reach Tagg and Tracer in Celadon city, having suffered some injuries on the way due to an encounter with the Zoroark impersonating Sabrina. He ends up losing an eye, but is determined to continue his mission.

Luke, Lake and Cinder go to the Nidoran colony in hopes of contacting Silent, but are captured by the Nidorinos. When they finally meet with him, all of them also discover that terrible things have been happening over at the PEFE headquarters. Luke manages to earn the colony's trust by showing them the Rainbow Feather, and thus heads with Silent on a mission to rescue the Nidoran specimens sent to PEFE's headquarters. Tagg and Tracer, as well as Wolf decide to find out what is going on at the headquarters.

Gamer's Feraligatr Typhoon manages to escape from the prison in Icirrus city before she can be locked away, and manages to track down Gamer. With some help from the Cubone tribe, the Resistance eventually begin setting up their new base in the Entralink. While Fool manages to defeat the Resistance force in Pinwheel forest, forcing them to escape, Napoleon the Emboar murders several of the Pokémon working for them, and makes it look like Fool was the one responsible.

Tagg, Wolf, Silent, Luke and some of their Pokémon, as well as Iron Marrow, after being gassed and captured, have to deal with an evil A.I. "PEFeDOS" that has taken over the facilities. They are separated and forced to run test tracks with space-warping technology, where Tagg meets this timeline's Tangent; after Silent unknowingly "cheats" and PEFeDOS attempts to kill him, he is left for dead but survives and, unmanaged, wanders around to discover the habitats and Basket. Silent learns about the Nidotoxin production facility and destroys it helping liberate the other groups. After the four groups meet and Basket awakens Tangent's memories, the entire group faces the evil A.I. and defeat it, then release the Pokémon held captive and proceed to restitute PEFE back to service.

Chapter 39: Darkest Hour

Fools' Houndoom and Skarmory take her to Pinwheel Forest while fleeing from the Pokémon now working for Napoleon, where Satine the Chandelure brings them over to the Entralink. Cuddlekins the Houndoom explains to Chase and Goggles about how Napoleon had been manipulating Fool all along. Unite's group is ambushed by Barb, Pollen and a team of bug types, who try to force Unite to give up the Light Stone by taking Woolly as a hostage. Unite ends up offering himself as a prisoner instead, and is captured by the bug types. Mira sends some Pokémon to retrieve the Dark Stone, but Portales gets there first and manages to obtain the stone.

Tagg, Luke and the others head over to Johto to expose the Zoroark gym leaders there. Fool regains her memory, and has a My God, What Have I Done? moment. Napoleon has defeated Mezzo's forces and taken over Black City, but Snowman helps them escape, while Shadow and Sunny meet with Every and eventually find their way back to the Resistance over at the Entralink. Napoleon attacks Nimbasa, and Star and Daisy break out Anom and Unite from the prison near the Moor of Icirrus. Mezzo regains her memory, and like Fool, has a My God, What Have I Done? moment. Tagg and Luke move on to Hoenn to expose the Zoroark Gym Leaders there, and discover that the Zoroark impersonating Norman is Phantom. Wolf and Crewe stay in Johto, where they discover that the Zoroark impersonating Pryce is also a Zoroark they already know, namely, Hecate. Crewe fully regains her memory, Hecate regaining hers as well. Unite and the rest of Luke's team head over to Dragonspiral tower, in hopes to awakening Reshiram.

Chapter 40: Recovery

Unite successfully awakens Reshiram, and she helps them start up with their plan to evacuate Unova before Napoleon can kill everyone. Reshiram also helps convince the Pokémon in Celestia's kingdom in Relic Castle to help, and Celestia regains her memory upon reuniting with her son Helios. Every tries comforting Mezzo, who is still upset about her actions before regaining her memories. Luke, Tracer and Tagg head over to Castelia to deal with the Zoroark impersonating Burgh, and end up in some trouble. It eventually leads to Skyarrow Bridge being blown up, and Lake being forced to jump off and swim to shore to get away in time. Tagg manages to sense that the Feraligatr is still alive via aura, but not where he is. While Luke and his Pokémon try to find Lake, Stratus shows up and meets with Lake.

Upon encountering Luke's Flygon Dusty, Stratus regains his memory as he remembers DS' Flygon, Jayna. This leads to Luke's Pokémon realizing how odd it is that no one has heard anything from DS ever since the timeline changed. Lake reunites with Luke and the others, and they continue working on the evacuation plan. Anom reunites with his team, including Yanmega, who was never killed in this timeline. It is discovered that Sunny is the Hero of Ideals, and Zekrom is awakened. Wolf and Crewe head over to Hoenn to meet with the human resistance, after finishing dealing with "Clair".

Anom and Tagg attempt to snap Fool out of her Heroic B.S.O.D., which leads to Fool stabbing Anom in the leg in anger due to a failed gambit on his part. After asking his Audino to help Anom, Tagg goes after Fool and eventually manages to convince her that her actions in the alternate timeline were not her fault.

Chapter 41: The Invasion of Pokepan

Scolipede orders three generals to invade Kanto (Lanius the Samurott), Johto (Rommel the Serperior) and Hoenn (Lelouch the Dragonite), in an attempt to regain control. Tagg, Luke and Tracer save the Gym Leaders from Quest island, and try to fight against the invading Pokémon in Kanto and Johto. Wolf brings Crewe to the human resistance base in a swamp near Mossdeep city, located within a submarine. They end up having to fight against the general along with Steven and Blue.

The Saffron-Celadon megapolis becomes a bloody battlefield, with many deaths in the very first days, whereas Goldenrod City is taken Rommel the Serperior's strategies, to then face the Nidoran army and other species in the vicinity they are recruiting. Reshiram and Zekrom decide to try to help Kanto and Johto and fly off to fight the invaders. Meanwhile Hoenn is swiftly overrun from the eastern sea. Tired of only laying in bed while his wounds heal, Anom decides to do something else. After helping Goggles regain his memory, Anom and Star leave through the space tunnels, ending up near the human resistance base, and joining them just before the submarine leaves for Unova. Every, Mezzo and Straw take a space tunnel to Kanto, and end up assisting Tagg and Tracer, while Fool goes to Johto and meets with the Nido colony that is helping Luke.

DS' Sinnoh team have been searching for the other trainers, and end up in the desert. Celestia's desert patrol finds them, and takes them over to the castle, allowing them to stay there for the time being. Napoleon continues trying to take over the cities of Unova, MGMT and Numbskull are able to distract Napoleon for a while with a dance party, the sheer awesomeness of Napoleon being temporarily defeated through the power of dance somehow freeing Slouch from his NPC state. Reshiram arrives in Johto, while Zekrom arrives in Kanto, to help the trainers fight off the invaders in those regions. Luke's Pokémon, with the help of Reshiram and the Oblivia Beasts manage to deal with the invaders, and between that and the underground guerrilla in Goldenrod causing unrest, Rommel meets with Luke and agrees to surrender and instead help them deal with Lanius the Samurott. Wolf, Anom, Crewe and Star meet with the desert patrol, and meet with DS' Sinnoh team. Luke, Tagg, Tracer, Every, Mezzo, Fool, and Straw deal with Lanius, and after a really tough fight, manage to defeat and capture the Samurott, and then cripple him so that he can no longer hurt anyone.

After helping some former minions of Lanius, whom the trainers had marooned on an island, they head over to Relic Castle to meet with DS' team. DS' team explain what had happened to them in the last few weeks, revealing that Cyrus is hiding out in the Giant Chasm, and has Celebi under his control in addition to Dialga. They also explain that DS tried to confront him, but failed, and was seemingly killed by Primal Dialga. Unbeknownst to everyone, Dialga managed to resist Cyrus' orders and sent DS to the dimension where the legendary Pokémon had been imprisoned instead of killing her. While DS and the Lake Trio are trying to find Palkia so they may escape the other dimension, Tagg, Luke and Tracer return to the PEFE base, discovering that the third general has somehow ended up there. The general is eventually defeated, and has somewhat of a BSOD upon meeting with his sister, who is shocked to discover what he has been up to.

Chapter 42: Dragon Down the Empire

After dealing with the invasion, the trainers eventually all meet up to take down Scolipede, Artemis and Napoleon. Goggles easily takes out the five Zoroark guards, but their Chatot partners get away and warn the others in the castle. Goggles and Chase lead the way as most of the trainers enter the castle. Bisharp prepares to execute some captured Pokémon, but some of Tagg's Pokémon try to deal with him. While Bisharp proves too powerful for them, they are eventually rescued by Escavalier, who shows up and manages to kill Bisharp after a sword fight between them.

Anom decides to go find Scolipede and attempt to restore his memory, while most of the others head over to the throne room. When they get there, they find Artemis laying on the floor, now a nervous wreck, while Mira and several other guards attempt to protect Artemis. Eventually, Napoleon shows up, and Mira tells the guards to redirect their attention towards Napoleon and his troops. Napoleon enters the throne room, along with his remaining minions and a fight breaks out. Napoleon attempts to kill Artemis, only for Mira to intervene, getting fatally injured in the process.

The others continue to fight off Napoleon's forces, while Artemis' ends up restoring Chase's memory by accident, allowing Chase to restore Artemis' memory, causing her to have a My God, What Have I Done? moment. Anom manages to find Scolipede and restore his memory. Scolipede orders everyone to escape from the castle as a giant Hydreigon is unleashed and flies towards Opelucid City. The trainers try to deal with the Hydreigon, while Crowbar with the help of Snowman summons the spirits of the Pokémon Napoleon had killed, which proceed to attack Napoleon and have the giant Hydreigon eat him. The trainers eventually manage to defeat the giant Hydreigon, and so Unova is finally free from Scolemis' rule.

Chapter 43: Loose Ends

Now that Scolemis is out of the way, all that remains is to take down Cyrus. However, before that can be done, there are some loose ends that need to be tied up first. Tagg prepares to go confront the Galactic admin he had fought before, and who had helped Cyrus escape the Distortion world and alter the timeline. A few more of the Pokémon regain their memories. DS' team inform Reshiram and Zekrom of Cyrus' whereabouts and of DS' disappearance. Wolf looks after Artemis, deciding to take care of her until DS is found. Pentigan returns to Hoenn, to meet with an old friend. DS and the Lake Trio finally find Palkia, only to discover that she has been turned to stone. This leaves the four of them having a hard time figuring out how they are supposed to escape, until they discover the Lustrous Orb nearby. Once having retrieved the orb, DS invokes The Power of Friendship to activate the orb's power and restore Palkia to normal.

Chapter 44: Time and Time Again

The trainers and their Pokémon head over to the Giant Chasm for the final battle. Things are quiet at first, but then several thick, thorny vines shoot out from the ground, and soon after Cyrus' Pokémon appear. However, taking them down proves difficult due to Celebi and Dialga assisting them using their powers to warp time. Pentigan manages to fully evolve, and goes inside Celebi's mind, helping restore her to normal, not before Reshiram and Zekrom have been restrained. Luckily, DS shows up with Palkia and the Lake Trio, having just escaped from the dark dimension and Mesprit and Azelf free Reshiram and Zekrom.

Lelouch shows up, geasses several of the trainers to not interfere, and proceeds to geass Cyrus, leading to Dialga becoming fully Primal. After Primal Dialga has been weakened, Tagg manages to use the Adamant orb to reach out to him, and restore Dialga to normal.

Palkia and Dialga reunite, and along with the Lake Trio begin discussing how to split the timeline in two so the original timeline can be restored without destroying the second one. They eventually figure out how to do this, and receive Arceus' permission to do so. After saying good-bye to their AU teams, the trainers prepare to return home, Dialga and Palkia warn them that since it is not only a difficult process, but also that they have never done it before, there might be some glitches. Palkia takes the Lustrous Orb back from DS, and she and Dialga proceed to separate the timelines and the trainers return to their own timeline.

Chapter 45: Homeward Bound

Finally the trainers have returned to their own timeline, but things have not exactly returned to normal. Some of the trainers suffer from the psychological effects from their experiences. In what has now become a proper alternate universe, AU!Tagg tries to gather the AU!trainers together to form a team like their OT counterparts. AU!Star goes to look for her parents. AU!Silent and Maekrite are summoned to the Bell Tower, then disappear. AU!Luke meets AU!Lake proper and welcomes him to the team. The recovery processes for Hoenn and Sinnoh begin. Cyrus has been imprisoned in the Distortion World once more, but is this time trapped within a time loop.

Back at the original timeline, the trainers start making plans for what to do in the upcoming weeks, including a vacation to the Orange Islands in about a month. During the time before they meet up again in Vermillion to go the Orange Islands, the trainers do various things. Several of them also pick up some new teammates during this time.

Aftershock Saga

The Orange Islands

Chapter 46: I Need A Vacation

The trainers meet in Vermillion and get on the boat to go on their vacation to the Orange Islands. The boat ride is mostly uneventful, apart from Phantom and Hallow having stowed away on the boat, and later discovering Entei on the boat as well. Anom getting pulled overboard by a Tentacruel that doesn't understand the concept of lungs, and managing to catch said Tentacruel before the others help him back onto the boat. And Tagg is still having trouble dealing with everything they went through in the AU, and doesn't react well when some of the others try telling him to get over it.

After arriving on Hamlin island, Phantom and Hallow begin pulling pranks on the hotel guests, such as stealing all their toilet paper. DS' Ducklett egg gets stolen by two Sneasel, and hatches shortly after Artemis and Mira, with the help of Luke's Gallade, Guardé. Artemis and Mira eventually decide on adopting the Ducklett, who is given the name Odette. Every's Pokémon get him into trouble again, forcing him to spend a few days working at a smoothie stand. Pentigan buys a submarine, not discovering until later why he got it at a low price. The trainers relax, enjoying their vacation. They meet with some new characters, and Every finishes working off his debt. Soon, the trainers decide to begin heading over to some of the other islands.

Elsewhere, a young Lugia is forced to flee when a Delta Feraligatr attempts to kidnap him for unknown reasons. The Lugia comes across Luke and his Pokémon, who protect the little legendary from the Feraligatr. Tagg starts exploring the places marked on a map he received shortly after arriving, finding some weird things in those places. When bringing the young Lugia Pleo back to his home, some of the Pokémon mistake Lake for the Feraligatr that kidnapped Pleo, and capture Luke and his Pokémon. Luckily, the misunderstanding is soon cleared up. Some more of the trainers end up getting involved in adventures similar to certain video games.

Chapter 47: Nothing Ever Goes According to Plan On Vacation

The trainers continue their various adventures around the Orange Islands. After fighting a Delta Rhydon, Luke and his Pokémon discover why the leader of the Delta Pokémon is after Pleo. Algira the Masquerain becomes a wanted mon among some wild Pokémon in the Orange Islands, for eating some of the smaller bug types on the island. One of the Pokémon belonging to Jenna, the trainer who caught Star, decides to steal the armband, and ends up accidentally dropping it, causing Rex to find it and discover its power. Rex is amazed by his transformation into a Spinda, and ends up telling his friend Lyra about it. Lyra also tries the armband, turning into a Smoochum. The two soon realize that it would probably be best to keep the armband's power a secret. Lyra and Rex later discover a flag tournament being held, and Lyra decides to enter, using Rex as one of three Pokémon in it. Star realizes the armband is missing when Jenna can't find it, and soon learns from Jenna's Squirtle that Jenna's Pidgey Ari was responsible for it. Jenna is also participating in the tournament, and eventually ends up in battle against Lyra. Before that happens, Star and Ari have a fight, with Star chasing Ari around and even evolving into Luxio. Shortly afterwards, they meet with Rex, and Star realizes he has the armband and explains her situation to him during the tournament battle.

Meanwhile, the other characters continue doing various videogame parodies. Rumours about Algira spread around the islands, leading to a bit of Gossip Evolution. An Impossible Thief Emolga steals the moon, leading to some slight chaos for a few days until the moon is returned when the Gardevoir thief the Emolga idolizes steals the moon back and puts it back in its proper place. A mysterious new trainer named Ori who seems to have a connection to the armbands appears, and joins up with the group. Ho-oh asks Luke and his Pokémon to meet him, and Tracer comes along. Ho-oh challenges Lake and a partner to battle him. Nadia joins him and the two actually manage to win the battle. As their reward, Ho-oh grants them some of his power, turning them into EX Pokémon. In the AU, most of the trainers head over to the Sinjoh ruins, where Arceus creates three eggs containing a second Dialga, Palkia, and Giratina. An odd occurance causes the mindscapes of several of the trainers (and Lake the Feraligatr) to blend together, and the various aspects of the trainers' personalities to discuss things related to recent and past events.

Rex decides to help Star return to normal, and decides to catch a Pokémon that he can trade to Jenna in exchange for Star. Luckily, his mother informs him that some Blitzle are up for adoption in the Johto Safari Zone, and he asks her to send him one. Lyra talks to Jenna for a while, until Rex brings the Blitzle over to befriend Jenna. The plan works, and Jenna trades Star for the Blitzle. After Jenna leaves, Rex releases Star, and she turns back into a human.

Chapter 48: Problems Know Where You Spend Your Vacation

DS and Anom defeat the leader of the Claydol that were hypnotizing the wild Pokémon of the island they were on, get their Pokémon back, and the Nanab berries that were stolen from the Aipom population are returned to them. They leave the island after one of the Aipoms joins Anom. Some time later, Pentigan gathers Star, Fool, Anom and Ori over for an experiment on a boat, which ends with Pentigan accidentally dropping his Gender Bender pendant into the ocean, leaving himself, Fool and Anom stuck as the opposite genders.

In the AU, Sol goes to do some research on Route 123. She gets captured by Unovan police and executed, coming back to life as a Banette. She asks AU!Tagg to train her so she can take a difficult challenge that can give her a chance to come back to life.

Afterwards, Crewe enters into a relationship with Jab, Every's Sneasel. Fool ends up with Majora's Mask, and begins to cause chaos across the islands. Luke and Tracer get attacked by the Delta Pokemon on their way back to the Orange Islands. The Delta Pokemon are defeated, and captured. Later, Every, Mezzo, and Straw go into the Dream World again after being told of a crisis between the Sun and Moon. Meanwile, in the AU, a glitch materializes in the Ruins of Alph and goes to explore the world taking the form of a Nidorino.

The Impossible Thief Emolga steals Tagg's cynical side, after overhearing a few conversations between him and DS previously. This causes Nihilist!Tagg to take control of him, and uses an aura connection to take control of his Pokémon as well. DS, Luke, Tracer, Anom and Every's Pokémon try to fight him off, with DS eventually putting two and two together and tracking down Emolga. After a long fight, they manage to get Tagg to fall asleep, allowing Emolga to return his cynical side and returning him to normal. DS catches the Emolga shortly afterwards to prevent her from causing any more problems. After getting his Pokémon back, Wolf is sent to deal with Majora!Fool, and manages to free Fool from the mask's control, before fighting Majora itself. After defeating it, Wolf and Fool reverse the curses cast on the islands by Majora!Fool.

Chapter 49: Every Vacation Has A Chance Of Turning Delta

A Delta Garchomp named Holly sneaks over to free the imprisoned Deltas and kidnap Pleo while she's at it. However, after freeing Ferno, he ends up accidentally alerting the others to their presence. Luke and Tracer's Pokémon attempt to fight off the Delta mons, but as they were still weakened from the fight with Nihilist!Tagg a few days ago, the Delta Pokémon end up winning the fight, and they get away with Pleo.

The other trainers decide to help Luke search for Pleo and spread across the archipelago, then they realize that Lugia himself is headed towards the Orange Islands when Tagg's Silver Wing begins to glow. Dividing into teams, the trainers begin searching for Pleo and the Delta Pokémon. Each of the trainers search the different islands, looking for clues and spreading the news, eventually finding some Delta Pokemon, but no sign of Pleo. While Silent and Kim spread the news among the wild population (not realizing they get mixed with the news from Algira and a "wooden monster" in an island), Rex finds a Delta Pokémon in the city.

Tempest, the Delta Feraligatr, and Thyme, the Delta Serperior, rescue Pleo while escaping the Deltas' hideout. Unfortunately, Pleo wakes up Ferno accidentally, forcing Thyme to hold the Deltas while Tempest escapes. Tempest eventually catches up with Luke, Tracer, and their mons, and head back to Shamouti Island to regroup with everyone.

While staying there, an evil version of Maxwell attacks Star, but she manages to defeat him using her strange notebook. A Delta Paras tries to infiltrate the group and attack Luke, but gets itself accidentally caught by Gamer. Meanwhile, Luke goes to meet with the Legendary Birds to let Lugia know Pleo is safe. Eventually, Pleo manages to contact his dad via Jello, and tells him he's safe. This results in the skies over the Orange Islands to clear up. Everything seemed to be going fine...

The day that Lugia is supposed to arrive to meet with Pleo, The Deltas sneak in and steal Pleo back, replacing him with a plush Lugia. When Luke and the others meet with Lugia, they realize Pleo was stolennote or, according to Woolly, TURNED INTO A PLUSHIE!!!. This makes Lugia go into a rage, forcing the trainers to fight him while DS searches for Pleo. She eventually fights the Deltas for Pleo, with help from Moltres and Fool. Pleo is won back and returned safely to his father, calming him, while Rex and Silent help hold back an invasion of Delta Pokémon at Shamouti Island.

Chapter 50: Vacation's End: Tricks, 'Tars, and Other Tomfoolery

After Pleo is returned to Lugia, Tangent sends out a text to everyone inviting them to a Halloween Party on New Island. All the trainers show up, some in costume, some not. Unknown to almost all of the trainers, Basket infects herself with the Charizard 'M virus. She infects other mons, and start to scare some of the others. What started out as a prank soon turned dangerous, as the infectees' begin to have the urge to infect the whole island. The remaining trainers and their mons fought off the infected, some having better luck than others. Thankfully, it was discovered that Lava Cookies and Full Heals cured the virus. The trainers then cure everyone and end the party, though many of them stay on the island, having nothing better to do. Pentigan finally gets his amulet back from Shift, and returns himself, then Fool and then Anom back to normal.

Eventually, Tagg and Tracer go to Knot Island, teleporting several others off of New Island to there along with them. Most of the trainers relax in the Hot Springs, while Tagg and Tracer teach Helios and Nadia how to hunt.

Tangent, Fool and Silent head to Shining Island to look for news about Basket's flock from Gaebora the Tropius. After Silent moves to Mandarin Island, Maekrite the Nidorino gets into a challenge with a local Nidorino that goes the wrong way, causing Ichtacya, who was checking around for Deltas, to attack him and end badly injured. As a result, Maekrite is banned from the island and Silent leaves to Tangelo Island.

In the AU, Sol has defeated most of the Midori mons, and is allowed to take a break and spend three days in the mortal realm. After the three days have passed, she returns to challenge the remaining four. AU!Tagg continues searching for the Nido, who is heading to Cerulean Cave, but goes for a brief visit to the OU to speak to Tagg. Upon returning, he briefly delays his search for the Nido to check up on AU!DS, who for somewhat unclear reasons had taken back the Lustrous Orb from Mt. Coronet.

After travelling through the Sevii Islands, and dealing with some Tyranitar after a fight broke out on Quest Island, most of the trainers head over to Hoenn; Rex returned to Goldenrod temporarily before rejoining with Silent in the Orange Islands, the latter planning to complete his challenge. Meanwhile, a minor character takes some of his Pokemon to Hoenn and Kim returned to Almia.

Hoenn

Chapter 51: Of Magma, Aqua, and Tortillas

Tagg has Xatu teleport most of the trainers to Littleroot Town. However, their trip to Hoenn doesn't get off to a good start when Tagg gets into a fight with Wolf over what happened back in the AU, putting nearly the entire group into chaos. After things calm down, the two manage to reach somewhat of an agreement. The next day, DS receives a phone call from Looker, who informs her that the former Team Galactic scientist Charon has been broken out of jail, but no one knows who did it, or why.

The trainers continue travelling towards Rustboro, several of them intending to take the gym challenge. However, not long after reaching Rustboro, some of them discover that Team Magma and Team Aqua are back, except this time, they are operating legally. However, as they are still causing causing ecological damage, Tagg decides to head over to Petalburg Woods to confront some Team Aqua members who are trying to expand the Route 104 lake. The protestors and some of the wild Pokémon are able to make Team Aqua back away for now, but doesn't make them give up on what they were doing.

In Rustboro, some of the trainers take the Gym Challenge, and some other stuff happens. Parisse has trouble with an unknown enemy, Pentigan puts a plan into action so he may later be able to go to Slateport without drawing unwanted attention to himself, and something strange happens to Fool when she tries experimenting with her obscura powers, and the orb she accidentally broke during the OI repairs itself in the process. Team Aqua makes another attempt at their project in Petalburg Woods, and Tagg and the protestors attempt to stop them once more. The Aqua Administrator at the scene, Ryklys, actually recognizes Tagg as a battler. Team Aqua eventually simply decides to just teleport them away.

As they begin to move on to Dewford, they find that Team Magma is now trying to expand Dewford, and Tagg ends up having his Pokémon dismantle the machines while the Team Magma member is distracted talking to him and Every. Later, Dewford gets attacked by a giant tortilla of all things, and the trainers fight it off. Team Magma and Aqua also fight it in an attempt to improve the public's opinion of them. During the battle, Crewe in her Sneasel form befriends some Pokémon, later discovering they belong to a Team Aqua member, who then accidentally witnesses Crewe changing back into a human when she drops her armband. While Wolf comes across a Team Magma member who has problems with Pokémon attacking her for no reason. He decides to let her try on an armband so she can learn to understand Pokémon better. Once the tortilla is defeated, a Gyarados shows up and takes the remains of it with it.

Chapter 52: J-Con

The group heads to Slateport and finds out that there's a convention about them called J-Con happening. Several of the trainers visit the con and meet many fans. Every ends up breaking a wax statue of himself, and ends up replacing it. The hall that he's in however, becomes enchanted by Mew so that anyone who enters it forgets about Every being in the J-Team. Wolf and some others find out about a fighting game featuring the group. Straw finds a fan impersonating him. Anom, after being attacked by a disguised Maylene, gets captured by one of his crazy fans, but manages to get free. Rex and Forte regroup with everyone via teleportation hax after Silent's victory over the OI's Champion: Drake.

After the convention, the group heads north to Mauville City, where some of them take on the Gym. Eventually, it is noticed that strange weather is happening over on Route 111. When they go to investigate, they find Jane, the Regis, and Jane's Pokémon trying to keep the route clear from Rain and Snow. With everyone's help, the route is eventually cleared- but not before Mew warps in some Fire types from Pokémon Island. They then head on over to the Lavaridge area to relax, challenge the gym and see Mt. Chimney. Kim reunites with Rex at this time, having been promoted to a Top Ranger position.

While that happens, Aqua, Rex's Vaporeon, and some of her partners, start getting ahold of Gems with weird properties. Silent sets some things in order at Goldenrod when without anyone noticing, Dintel is taken to the netherworld.

Chapter 53: The Reveal

There they find that much of the water there has been drained by the new Team Magma, causing serious problems for the Water-type population there. Mew attempts to fix the situation by turning Goldeen into Zubats; then meets up with the group and starts explaining things. Mew reveals that she has been messing with things in a manner similar to what happened with the Goldeen. As more Trainers gather there, Mew identifies one of them and reveals that Crewe is an orphaned Sneasel turned into a human. This comes as a big shock to everyone. Mezzo, despite efforts, falls into a very deep sleep due to a curse from Mew, and Pentigan receives the exact opposite curse, insomnia.

The group meets Crewe's aspects, but she is not interested in opening up and tries to force the group out. They accidentally end up in Pentigan's mind instead. With this development the Trainers's bodies remain in induced stasis, and it is up to a group comprised of Luke, Silent and Faith, plus some of their mons, to take care of them while Tagg attempts to bridge the mindscapes and the real world again.

Some of the Trainers start visiting each other's mindscapes, starting with Pentigan, then Mezzo, Rex, Star, DS, Straw, Fool, then Tagg, meeting different aspects of the Trainers and different challenges along the way. While that happens, Every's body is returned temporarily, triggering a brief skirmish between Every's mons, Maekrite and Guardé. Shahinne gets a hold of many Elixires, triggering a Double Team Apocalypse. Because of all the stuff going on however, the presence of the group at the inn is not well received. Silent and a team leave the town and head to Mirage Tower to go search for Dintel, only to find the tower guarded by Team Magma.

The characters in the mindscapes have some of their personality aspects randomly emerge on their bodies and promptly causing sillyness all around. Every's body is handcuffed to a bed by a stalker and his mons try to release him by all means. Luke, Tracer and Silent find out Team Magma has taken over Mirage Tower to protect the Pokémon there as well as try to acquire evidence against Team Aqua because of a weather manipulation machine; unfortunately, the adventure ends without finding Dintel and with the destruction of the tower. Shahinne and Every's "Dratini" Zubat get lost in Salamence's hyperspace plumage and then they fight some parasite mons, whom they must defeat to protect Salamence's health. The "Charizard ’M" aspect of Baskets tries to "infect" the people in the hotel, but ends up causing a "Tropius ’M" situation. Finally, T appears with some Unown friends and teleports Every's body to... somewhere, and now Every's team must wander around the city trying to find him. Odette meanwhile realizes what a Dream World's Pokémon fate can be and, worried, goes around looking for information about the DW.

Chapter 55: Holidays and Pokeringers

For the delayed celebration of the holidays, the Trainers start exchanging gifts, most notable of them a series of eggs given by Fool. For a different Xmas, Dintel is taken to the Netherworld by the multiverse's MAFIAA... until they are fed up of him. He is returned to Goldenrod where he is finally found by Sol. Pentigan goes around giving inadequate gifts to pretty much everyone.

The Trainers start leaving Fallarbor Town to different destinations, only to find as they go that no hotel across the region will host them any longer - they have concerted to not take them as guests to avoid the egregious property damage. Because of this, Luke, Rex, and Tagg's teams resort to making use of the Secret Base system. While in Fortree, a number of events occur, including the introduction of Umbra, Jeff, and 49 to the group, and Gamer's Smeargle Meme revealing that in fact he's not insane and is in fact part of an evil family of Smeargle, The Family of Blood, and challenges Gamer to a battle within Navel Rock. Gamer, Umbra, Jeff, Tagg, and their Pokemon teleport over there and end up not only defeating the Smeargle, but obtain a new move in the process.

During their stay, the Trainers end up getting involved in a Pokeringer competition in order to obtain a trophy with the Jade Orb embedded inside. It quickly becomes a Gambit Pileup as Teams Aqua, Magma, and Ozone, fringe elements of the first two teams, agents of Charon, and our heroes compete for the Orb. Unfortunately, Jet, a Team Ozone Admin, ends up winning the tournament by defeating Wolf, but the Orb is stolen from him and ends up in Every's possession. Wolf and DS also have an encounter with the Team Magma grunts Sierra and Vyvyan, who have been investigating the unusual weather. When Vyvyan reveals he has known all along of Sierra's ability to speak to Pokémon, and Sierra is unable to tell him why because she promised to Wolf to keep the armband a secret, Vyvyan runs off, believing she doesn't really care about him. Luckily, Wolf clears up the misunderstanding, and tells him about the armband. Sierra and Vyvyan help gather some information on a weather machine found on Route 120, after receiving a letter from a Swellow explaining Team Magma's findings at Mirage Tower.

Chapter 56: Perfect Aqua

While heading down Route 120, Sierra and Vyvyan come across a rather odd Absol, that Vyvyan ends up catching. The Absol leads the two to Team Aqua's hideout, where Vyvyan comes across Depthcharge, a clone of Kyogre. Already having found a clone of Groudon in Team Magma's old hideout earlier, Vyvyan is understandably unsure of how to keep two young legendaries under control, and Anja's claims of Vyvyan being "doomed" doesn't really help. Vyvyan's Gardevoir is also unsure what to do, but advices him to continue going on like usual, and enjoy his time with Sierra. Tagg picks up on the presence of Buggle (the Groudon clone) while teaching Fool how to make pokeblocks, and confronts Vyvyan about it. Later, while Vyvyan and Sierra are making a secret base, they notice that Vyvyan appears to be going through some odd changes, as he is unknowingly starting to transform into a Rayquaza from having to keep Depthcharge and Buggle from fighting.

Meanwhile, Aqua the Vaporeon is playing around, when the elemental gems which were enchanted by Mew suddenly absorb into her body, turning her into a giant Vaporeon shaped water monster. Some of the trainers, not realizing who the water monster is, try to fight her, until the gems separate from her and she returns to normal. While recovering at the Pokémon Center from the incident, she is taken by some rogue Team Aqua members, and some of the trainers have to go rescue her. After doing so, Kim decides to send her back to Almia with her mother Blossom the Leafeon for a while.

Meanwhile, Umbra's Sableye, Styx, reveals she's his reincarnated sister after they survive a nearly deadly initiation to the PEFE.

While walking around Lilycove, DS and Odette get attacked by two Rotom, which leads to Odette getting separated from DS where a foreign Salamence tricks her and tries to kidnap her. Odette ultimately manages to save herself, just as DS, Wolf and their Pokémon show up. During the battle with the Salamence, Odette evolves into Swanna and manages to win her battle.

Pentigan, who had been stuck in a "Freaky Friday" Flip with Susan because of a magic artifact, which then broke, is finally switched back to his own body after Landorus repairs the artifact, revealing that he knew very well of what had happened to them despite them trying to keep the switch a secret.

Team Ozone search for Vyvyan in order to speed up his transformation into a Rayquaza, and Anja the Absol, in a rather Jerk Ass move, uses Perish Song to knock out Vyvyan, Sierra and their Pokémon, allowing Ozone to easily get away with Vyvyan and bring him, as well as Depthcharge and Buggle to their lab. Sierra goes to DS and Wolf for help, who inform some of the other trainers. Having recently learned that the cloned Kyogre and presumably the Groudon were created from humans who lost their memories after transformation, they quickly figure out just what Team Ozone intends to do to Vyvyan. Anja shows up, revealing that Vyvyan isn't the first trainer she has allowed to walk into his doom, and tells Pentigan that something bad will happen to him sometime in the future. Pentigan begins trying to find Ozone's hideout, and more weather related weirdness continues happening more frequent in more parts of Hoenn.

Chapter 57: And Then Vyvyan Was A Rayquaza

After a few days, Team Ozone's leaders discover what their scientists have been doing behind their backs, and head over to the lab as Vyvyan, now a Rayquaza, awakens to find himself in a tank at Team Ozone's lab. Unlike the Groudon and Kyogre clones, Vyvyan's mind and memories are intact, and he understandably freaks out and starts trashing the lab, until he remembers Sierra and escapes by breaking through the nearest window to go find her. Sierra, her Pokémon and Vyvyan's Pokémon go look for Vyvyan, and they soon reunite. However, Vyvyan realizes that Depthcharge and Buggle are still in Ozone's hideout, and realizes he and Sierra will have to head over there later to rescue them. Pentigan comes across them, revealing that while he hasn't yet found the hideout, he has some idea of where it might be: in the sky. He also tells them that just like armbands that turn humans into Pokémon, there is armbands that have the opposite effect, and they head over to Mossdeep to find Susan and Latias so they can borrow one of the Pokémon-to-human armbands.

The armband allows Vyvyan to turn back into a human, and he and Sierra confess their feelings for eachother, deciding to go on a date while Vyvyan is human, unsure at the time if they'll be allowed to keep the armband.

Mananging to track down a weather machine that is making it hail in Mossdeep, Icicle the Glaceon tries to find a way to make it create snow, while Forte, Pianis and Katie try to figure out how to destroy it. Their attempts cause several other bizzare weather effects, even making it rain, hail, harsh sunlight and a sandstorm all at the same time, which causes Tagg's Castform to get sick. Along the way, Tagg heads over to the same ruins from before and gets another vision from the Unown about a disaster in Sinnoh and a very weird Reuniclus. They eventually manage to destroy the weather machine, and shortly afterwards, Leaflet the Leafeon runs away, believing his father Icicle cares more about snow than he cares about him. Leaflet comes across some Pokémon belonging to a Team Magma member that he gets along with, but Forte and his Pokémon eventually track him down and after a brief fight due to one of the Pokémon not being patient enough to talk things out, Icicle and Leaflet manage to talk things out.

Tagg heads over to Ever Grande to explore, bringing some of the other trainers along on an adventure in a place containing shrines to certain legendaries, and an old tomb in which they're eventually chased out by a different variety of Cofagrigus.

Team Ozone's airbase appears above Mossdeep, and Jet takes control from Archie and Maxie, who are revealed to be the leaders of Team Ozone, having formed it in an attempt to make a ridiculous team to discredit the revived Team Aqua and Magma, but lost control of their members. The two are locked up in the Cargo bay, as Jet begins looking for Rayquaza!Vyvyan. Pentigan's Zoroark and DS' Chatot have snuck aboard the airship, and manage to steal some information from Team Ozone's computers. The Latias sisters help Sierra and Vyvyan put up a distraction by disguising herself as Rayquaza!Vyvyan, and keeping the Ozone members' attention on her while the real Vyvyan flies up to the airship with Sierra, breaking into the Cargo bay, where they end up discovering Archie and Maxie's involvement with Team Ozone, and break the shackles put on them before going off to find Depthcharge and Buggle.

Thanks to the Pokémon trainers creating multiple distractions, Sierra and Vyvyan manage to get Depthcharge and Buggle back with little resistance, and the airbase eventually crashlands in the ocean when Artesia blows up part of it. Jet manages to escape, lamenting how his plans were ruined, only to remember the advice another Ozone grunt gave him regarding Rayquaza!Vyvyan having kept his memories and how Sierra could probably be used to get him to assist Team Ozone in exchange for her safety, and decides to make a new plan. After talking to the Latias sisters and being told they may keep the armband, Sierra and Vyvyan go to find Archie and Maxie, and Sierra confronts them about Team Ozone. After exchanging phone numbers, they agree to let eachother know if anything related to the weather machines or Team Ozone comes up.

Chapter 58: A Volcanic Finale

Gamer throws a party celebrating the first anniversary of the group getting together. Over the next few days, increasingly darker clouds begin gradually filling the skies of Hoenn. Jet attempts to kidnap Sierra, but with the help of Styx and some of her teammates, Vyvyan manages to save her. The source of the clouds is eventually tracked to Mt. Pyre, where Charon has been hiding out, with his biggest weather machine. Some of the trainers, as well as Sierra, Vyvyan and the other two cloned legendaries, as well as eventually the original Rayquaza head over there to deal with Charon. Realizing they can't just destroy the weather machine, as it might trigger the caldera Mt. Pyre is on the tip of and set off an volcanic eruption that could destroy all of Pokepan, they decide to try to deal with Charon and his many Rotom, and find a way to safely disable the machine. Meanwhile, Silent, Pikaninja and Artesia are in Mauville, where it is discovered that Charon has been taking energy from New Mauville.

After fighting off several of Charon's Rotom possessing mechas, Looker shows up to arrest him. Panicking, Charon attempts to try something with the weather machine, only to accidentally trigger the caldera instead. The trainers try to deal with it, as well as the others outside of Mt. Pyre helping with evacuations. Eventually, the weather trio decide to do sacrifice themselves to stop the caldera via an ancient ritual, but the mini weather trio decide to help as well, and with their help, the caldera is stopped without the death of either weather trio. Worn out, the original weather trio decide to sleep for a few days to regain their strength, while letting the mini trio temporarily be in charge.

Chapter 59: Emotion (Sinnoh) / Tutelage (Kanjoh)

The group ends up splitting up for a bit, with some going to Sinnoh and the others to Johto.

The Unown's prediction to Tagg comes true as the mysterious Keystone inside his backpack turns out to be the Soul Jar for the Obscura King that ruled Sinnoh about a millenium or so ago. Tagg tries fighting against him after being separated from his Pokemon and manages to wound him, but ends up getting a Dark Pulse to the back for his troubles and ends up being saved by his Pokemon, albeit severely injured. The Obscura wizard then uses his powers to cover Sinnoh in a twilight haze that reduces the majority of the population into mere wisps, and cause a mass release of Spiritomb as well as killing off most electronics.

After making it back to DS' house, Tagg and his Pokemon soon figure out that they're invisible to most other people, and once they manage to get DS and Wolf's attention, Tagg ends up falling unconscious and has to be carried inside. At around the same time, the airship group ends up crash-landing in Sinnoh due to electronic disturbances mentioned earlier. During this time, it's revealed that Souls of Silver appear to have a resistance to the Twilight, as they don't become wisps. Once most of everyone gets back together, part of the group heads over to Mesprit's cavern to see what exactly is going on. Mesprit reveals that in order to free Sinnoh from the twilight, the trainers have to find Tears located all over Sinnoh, starting with her own in western Sinnoh. The trainers then fan out to look for them.

Umbra and Lina meet, discovering their shared abilities and longevity. Despite a rough start, the two eventually form a relationship. Meanwhile, Umbra catches a rouge Spiritomb who's a Soul of Silver, and Lina obtains a mysterious Alakazam. The two are also joined by Gene and his Pokemon.

Rex continues his Gym challenge, despite the power outage, eventually obtaining Candice's badge.

The Morendo family discovers that Sunny is a Soul, and he is promptly used to help the Morendos not get wisped in the twilight.

Eventually, all but one of the Tears are collected, and there is a massive boss battle against a giant Armortomb. After it is defeated, Mesprit restores her third of Sinnoh, and the team takes a break before moving into the next section.

Meanwhile Tangent has got himself trapped in Mirage Island together with a Sneasel!Poacher and Vyvyquaza, and Ílex Celebi sends Silent there to rescue them. After that, Silent moves to Johto to help deal with the public relationships of PEFE and the J-Team. He finds himself joined by several mons from other trainers, and eventually ends up splitting his team, leaving Maekrite at the Goldenrod Colony to train both Pierce and Teala while Roc goes to visit Shahinne's bird family. A group of Trainers accompanied by Steven and a mysterious Incognito character roam the eastern side of Johto, and Straw manages to survive a shipwreck in the Whirl Islands, although he is later believed dead. Tracer and Luke arrive to Johto by different means, only for the Johtoan trainer to be suddenly confronted by Suicune, who challenges Luke to a battle at a future date.

Chapter 60: Willpower (Sinnoh) / Spring Training (Kanjoh)

The Sinnoh group heads into the next section to speak with Azelf. While collecting Tears, at one point they end up getting ambushed in Hearthome by a group of Spiritomb, but get saved thanks to the efforts of some old friends first met during the AU. Another important event that occurs is Forte getting his arm broken by getting it smashed by an Armortomb's mace. At the end of the Tear hunt, the group ends up fighting the Sinnoh branch of the Family of Blood, who anger Tagg enough that after beating them he summons Groudon to drag them all to an ambiguous fate. In the interim while preparing to head up north to Uxie's section, part of the group heads over to the Cubone tribe to use the time tunnels in order to discover the backstory of the Obscura wizard.

Chapter 61: Knowledge (Sinnoh) / ???? (Kanjoh)

In Kanjoh, some of the trainers return to Goldenrod for various reasons; Jeff has to begin his application for PEFE while Lazy Latios scares a Murkrow murder away, revealing himself in the process.

Meanwhile in Sinnoh, one of the groups spearheaded by Tagg meets a very distrusting pack of Lucario in the wild and try to convince them to hand over a Tear. During April Fools Day, weird events happen once again, but more Tears manage to be collected. For the last few Tears, the group spearheaded by Tagg ends up getting spirited away to Gracidea by a group of Obscura users to find them amongst the flowers. Umbra ends up dueling with their leader in order to get the very last Tear of the region, and succeeds after a close battle. After Uxie manages to remove the Twilight from northern Sinnoh and the group recieves the Emblem Of Knowledge, the group heads once more into the time tunnels to see how Annoski managed to get sealed.

Chapter 62: The Twilit Endgame (Sinnoh)/ ????? (Kanjoh)

Afterwards, the group ends up heading to three locations: Sendoff Sping, The Flower Paradise, and Alamos Town in order to place the Emblems given into the right spots. Once that is completed, lights from the Emblems fall over the same ruins where Tagg released Annoski in the first place. Once he puts the Adamant Orb in a special slot, time is rewound and the ruins are restored to their original state, a massive tower. Lina, Tagg, and Pentigan end up fighting the souls of the Aura Guardians in order to open a door, where the three face everyone while within a giant robot. After that, our heroes manage to find out Annoski's location, a cathedral to the north of the Battle Zone.

Everyone teleports there, but Tagg and his Pokemon are forced to go it alone due to Annoski threatening the safety of his friends with the Wondertombs he'd saved just for last. The next morning, Tagg's group infiltrates the Cathedral and confronts Annoski and his personal Spiritomb, being joined by the others soon afterwards while the Aura Guardians hold off the Spiritomb reinforcements. After a tough battle, the Keystone is shattered, reducing Annoski to a spirit, who is then taken away for judgement. The Sinnoh group then returns to the Resort Area to rest and recuperate, where they meet a trainer named Eskay, who had gotten stuck in Sinnoh during the twilight.

Soon afterwards, hints start being made about returning to the Pokemon-only world...

Paths Saga

Pokemon Mystery Dungeon Returns

Chapter 63: Brave Not-so-New Worlds

Most of the group ends up traveling to the Pokemon-only world using the Entralink. Before leaving for the PMD world, Wolf discovers Anom has been kidnapped by some people for ransom. Anom is eventually broken out, and taken to PMD with Wolf, Tangent, and DS. Eventually, most of the group finds out that the orb at the top of Destiny Tower has been shattered, scattering shards of it across the world, some across universes. Some members of the group discover that the shards have the power to teleport people and mons across universes. This results in several people leaving and entering the PMD world.

Chapter 64: Here and There and Everywhere

On the PMD-B side of things, part of the group ends up exploring post apocalyptic Kanto together, Tagg finding a mysterious holotape in the ruins of his household. Following some misadventures they all end up in the former PEFE HQ, meet an AI by the name of Cornn and end up accidently reawakening PEFeDOS, who makes them do more insane tests, until Cornn end up taking control of her stand and pulls a Face–Heel Turn. After managing to defeat Cornn and stop a meltdown of the entire facility, PEFeDOS decides to forget about taking her revenge, and the group manages to fully listen to AU!Tagg's message, leading Tagg and his mons to head over to Angela in search of the surviving humans and the Brotherhood of Steel, whereas Tracer's group decides to stay in their portion of the world for a little longer.

At around the same time, Abigail and her new Flygon friend Rojos end up getting involved in the politics of the region of Hoenn known as "The Bay", and the newly christened Team Nova explores post-apocalyptic Johto, encountering various different civilizations as well as Mystery Dungeons created by the power of the shards, as well as consorting with Daedric Princes visiting from other worlds.

Chapter 65: Bloodstained Sands and Malarial Tides

In Angela Tagg and his group end up tangling with the Unity, a group of mutants dedicated to making the entire world like them, as they attempt to help a human known only as the Vault Dweller recover a water chip. Compounding their problems is the fact that due to a Raider attack upon arriving in Angela, Tracer and a dictator Archeops from the Empire of the Ancients end up switching bodies. At the same time they meet with the AU versions of Alistair and Wolf, the latter a shell of his former self following DS' death, in search of the Adamant Orb in AU!Tagg's possession in order to change the results of the dragon war. Following the defeat of the Master and his Lieutenant, Tagg and Cobalt reveal that they always knew about the body swap, and they end up heading to Alto Mare, now known as Almer, via space tunnel in order to get Tracer back. Before then though, AU!Wolf dies sending a message to the past in order to stop the events leading to DS' death.

Meanwhile in Hoenn, Abigail is forced to come to terms with mutating into a weresow due to an accident in a Hoennese science lab, while Team Nova ends up arriving in the region in search of her.

Within Almer, Tracer ends up signing a deal with the Hoennese Emperor, but the group ends up in a battle with the emperor's forces once he manages to get back in contact with them, leading Xatu to send them to a side universe of kaiju mons using the shards after Tracer gets his body back. Afterwards Tagg and Tracer's groups end up fighting...something before the Time Space Orb is restored to its former glory, and Team Nova gains knowledge of the Alakagross civilization.

Kanjoh- 2

Chapter 66: Breather Arc

The J-Team members decide to basically take a rest while collecting badges in Kanto and Johto. A not so relaxing event involves the members of PEFE and some other J-Team members taking on various Pokefutures experiments in a PEFE HQ that has lost power and is in danger of collapsing.

Cipher Saga

Unova- 2

Chapter 67: We're in Unova Again!

The J-Team heads to Unova after hearing about Pokestars from those who had gotten there earlier, eager to participate. Some trainers decide to give the Unova League Challenge a try while some are forced to redo it due to their trollish psychic birds.

Chapter 68: Twin Worlds

When Pokemon from the Dream World start pouring into the real world for seemingly no reason, the J-Team searches for answers, eventually finding the answer in the form of a briefcase machine which can be used to close rifts, even if only Tagg has one at the moment. More people decide to take the League Challenge and retrace their steps to face the Gyms the rest of the group already moved on from.

At the same time, Deimos, a former Team Galactic Commander, meets and tries to kill the J-Team on several occasions.

Chapter 69: Not So Beautiful Dreamers

The Dream Rifts start getting worse as two rifts appear simultaneously in Reversal Mountain and more appear across Unova. Thankfully, more machines arrived recently, so people other than Tagg can help close the rifts, too. Meanwhile, the mysterious gold and silver Bisharp, Edge, becomes an increasingly annoying threat, after kidnapping Carol to hapazardly assaulting various team members. It is soon agreed upon that he needs to die, and during a final showdown in Humilau, Edge is killed by Herbert. Those of the team working on challenging the Gyms work to get the last of their badges and head to the League. Around the same time, the smuggler Melinda is stopped after she kidnaps DS and Mirage once they figure out her true identity.

Chapter 70: League Challenges and More Dream Rifts

The J-Team members challenging the Unova League do so, with many becoming winners, but others becoming losers. Titan ends up taking a Dream Rift machine from Herbert, and the J-Team ends up having to reseal Dream Rifts throughout Unova following revelations from Cresselia, culminating with the largest at the Entralink.

Chapter 71: Postgame

After the rifts close, the J-Team does various things, such as exploring the parts of Unova they haven't yet, challenging the PWT, meeting up with old faces, or just hanging around in one location for a long period of time. Near the end of their time in Unova, it is discovered that the scientists that injured Cresselia have a base of operations in Holon, and the J-Team moves there to track them down.

Holonquest

Chapter 72: Lost in Time

The Team arrives in Holon. Ammy, Tagg, Herbert, and Issun are sent back in time ~600 years and begin fighting against demons plaguing the land while said land gets ready for war.

Chapter 73: Following the Thread

The J-Team discover there are Pokemon that have been experimented on that have multiple types and head for Holon City to take care of it.

Chapter 74: Of Science and Ghostbusting

The J-Team get a move on and do various things, including out the scientists doing the multityping experiments. On the Conquest side of things, the war starts wrapping up and Umbra is deposed.

Chapter 75: When Ciphers Attack

The Okamiquest group returns home. Duke is snagged by Alexiel and Crow is hospitalized by Verax. Tokarev appears and is revealed to be the Cipher operative from Tagg's mindscape. The group heads to Orre following a text war.

Orre

Chapter 76: Ready Orre Not

The group arrives in Orre. Various Pokemon are Snagged and Shadowed. Crow and Psyche try infiltrating Cipher, the latter having more success than the former.

Chapter 77: The J-Team Strikes Back

The group manages to do a raid on Snagging and Distribution. Bishop starts hosting Support Group meetings for current and former Shadow Pokemon. Diane and other Shadow Pokemon are purified. Paula snags and Shadows Heatran.

Chapter 78: Unwelcome Revelations

Alexia is revealed to be Lyuri. Titan's Lab is raided. Crewe comes back to the group. Resources is raided.

Chapter 79: Cipher's Last Stand

R&D is raided. Mindscape shenanegins. Special Acquisitons and Operations are raided.

Chapter 80:

Neo-Galactic becomes a thing. Tagg leaves the team to go find himself and to protect them from the fallout of the Very Bad Thing. Fairy-types become a thing. Jacob snags Regina back. Maggie goes to try and find Tagg. Eskay leaves the region. Herbert leaves to try and find Tagg.

Recovery Saga

Kalos Arc

Chapter 81: C'est pas le Pokérou

After heading to Ecruteak for celebrating Christmas, the J-Team heads to Lumiose City in the Kalos region. Alyssa joins a group which makes itself known as the Illusion Project.

AU Arcs

Return to AU: The Draconic Uprising (Part of the Paths Saga)

The AU cast tries to take down a clan of Dragons wanting to turn all humans into Pokemon.

Community

Tropes HQ

TVTropes is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Permissions beyond the scope of this license may be available from thestaff@tvtropes.org. Privacy Policy